Chronological, Gestational and Biological DNAm Age Estimation with Methylation-Based Clocks

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Documentation for package ‘methylclock’ version 1.99.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS

Help Pages

ageAcceleration	Epigenetic age acceleration, intrinsic and extrinsic
ageAccelerationChen	Chen-style extrinsic age acceleration with data-driven weights
anti_trafo	Horvath age transformation (inverse)
as.data.frame.methylclock	Coerce a methylclock result to a data frame
cellCounts	Estimate blood cell-type proportions from methylation
clockAccuracy	How well each clock tracks chronological age
clockCoverage	CpG coverage of each clock in a dataset
clockTrajectories	Arrange repeated samples into per-subject clock trajectories
clock_catalog	Catalogue of the clocks in the package
clock_info	Look up one clock's registry entry
clock_list	List and filter registered clocks
clock_predictors	Supported prediction engines
clock_register	Register a clock
clock_registry	The clock registry
clock_reset	Clear the clock registry
clock_statuses	Availability status labels
clock_targets	Supported biological targets
compute_clocks	Estimate clocks from a methylation matrix
DNAmAge	Estimate chronological and biological DNAm age
DNAmGA	Estimate gestational DNAm age
EEAA	Extrinsic epigenetic age acceleration (canonical EEAA)
IEAA	Intrinsic epigenetic age acceleration (canonical IEAA)
imputeKNN	KNN-impute a methylation matrix
listCellReferences	Cell-type reference panels available for deconvolution
mcd_backends	Configure the resource backend chain
mcd_cache_clear	Clear the resource cache
mcd_manifest	The resource manifest
mcd_resource	Resolve a clock resource by identifier
mcd_resource_file	Resolve a file resource to a local path
mc_to_hdf5	Store a methylation matrix on disk as HDF5
methylclock	Estimate DNA methylation clocks
methylclock_betas	Example methylation beta matrix
methylclock_cells	Clock estimates with blood cell proportions
methylclock_demo	Example clock estimates for a public blood cohort
methylclock_longitudinal	A longitudinal example: children sampled repeatedly from birth to age 3
methylclock_references	Clock estimates on the shipped reference cohorts
methylclock_smoking	Smoking predictor scores with smoking status
methylclock_validation	Clock estimates on two independent validation cohorts
new_methylclock	Construct a methylclock result
normalize_coef	Normalize a coefficient resource to canonical form
persist	Persist a result to a file
persist.methylclock	Persist a result to a file
plotAccelerationByGroup	Plot epigenetic age acceleration by a sample group
plotAgeAcceleration	Plot epigenetic age acceleration
plotBlandAltman	Bland-Altman plot of predicted vs. chronological age
plotClockCorrelation	Heatmap of the correlation between clocks
plotClockDensities	Plot the density of each clock's estimates, optionally split by a group
plotClockDistributions	Plot the distribution of each clock's estimates
plotDNAmAge	Plot predicted epigenetic age against chronological age
plotGroupDifference	Plot the per-clock difference between two groups as a forest plot
plotReferenceRange	Plot samples against the percentile bands of a reference cohort
plotSampleDiscordance	Plot how much the clocks agree on each sample
plotSamplePCA	PCA of samples in clock space
plotTrajectories	Plot each subject's clock trajectory over age
qcReport	Quality-control report for clock estimates
sampleQC	Per-sample quality control
theme_methylclock	A clean theme for methylclock plots
trajectoryRates	Each subject's rate of epigenetic aging, clock by clock